rada16-geometry

RADA16 / SAP geometry + in vivo kinetics — validated parameters

Source agent: Domain 4 (Sonnet 4.6), 2026-04-23. Consumer: hydrogel_phase4d_factin_bundling_model.py (scaffold geometry) + hydrogel_phase4e_cochlear_pkpd.py (gel clearance).

Parameter table

Parameter	Literature value	Source	Status	Used in
Antiparallel β-sheet H-bond spacing	4.7 Å (0.47 nm)	Cormier 2012 Biomacromolecules (WAXD, paywalled abstract); amyloid standard	✅ primary	Phase 4d fibril math
Peptides per nm fibril axis (derived)	4.26/nm (bilayer: 2 peptides per 0.47 nm step)	2005-yokoi-kinoshita-zhang-rada16-reassembly + Paravastu 2014 double-sheet model	✅ derived	Phase 4d RADA16_MONOMERS_PER_NM_FIBRIL
Single nanofiber dimensions (tape)	3 nm wide × 2.5 nm high (flat, 2 β-sheets, alanine core)	Paravastu 2014 ACS Nano (PMC3946435, solid-state NMR)	✅ primary	cross-section context
Bundle diameter (EM observations)	10–20 nm (aggregated ~3–7 individual nanofibers)	1993-zhang-eak16-rada16-spontaneous-assembly Zhang 1993 PNAS 90:3334	✅ primary	bundle vs fibril distinction
Mean fibril length (AFM intact fibers)	615 ± 104 nm	2005-yokoi-kinoshita-zhang-rada16-reassembly	✅ primary	—
Mean fibril length (pH 4.5, end-to-end assembly)	296 ± 131 nm	PMC3318125	✅ primary	pH-dependent
Observed fibril length range	200 nm to few μm	2005-yokoi-kinoshita-zhang-rada16-reassembly	✅ primary	Phase 4d fibril_length_nm = 1000 upper-range
β-strand axial tilt	~35° from fibril axis (2-residue registry shift, Class 3R2)	Paravastu 2014	✅ primary	—

In vivo PK (assembled RADA16 gel)

Condition	t½	Source	Notes
Rat liver injury (uncrosslinked RADA16)	3–7 days visible; dissolved by 14 days	2021-frontiers-rada16-clinical-review (PMC8216384)	Direct histology
Rat TBI brain (uncrosslinked)	Visible at 7 days; absent at 21 days	2021-frontiers-rada16-clinical-review	Direct histology
Crosslinked RADA16 variants	61% degraded at 35 days	2021-frontiers-rada16-clinical-review	Extended persistence
Derived assembled gel k_dissolution	0.002–0.004/h (t½ 7–14 days)	0.693 / (7–14 days × 24 h)	calculation
Free monomeric 16-mer in serum	~30 min plausible (not measured directly for RADA16)	General small-peptide serum stability	inferred

Tail-length modification limits (h09-critical)

Empirical assembly limit for appended sequences onto RADA16:

Appended length	Assembly behavior	Source
≤12 residues	β-sheet assembly preserved	2021-frontiers-rada16-clinical-review (Frontiers 2021 review, PMC9739689 citations)
12–50 residues	Monotonic reduction in viscoelasticity / β-sheet signal	Same review
ALK-tagged RADA16 (+3 hydrophobic residues)	Rapid collapse to spherical aggregates	Same review
>50 aa globular domain	Never tested in published literature	—
Our tail91 construct: 118 aa	UNCHARACTERIZED, ~10× beyond empirical limit	—

Red flags in current h09 Phase 4d/4e model

Model constant	Value	Problem
RADA16_MONOMERS_PER_NM_FIBRIL = 4.35	comment “Zhang MIT”	Value defensible (2% off 4.26). Comment misleading — Zhang 1993 provides no such number. Correct citation: Cormier 2012 (WAXD H-bond spacing) + Paravastu 2014 (bilayer model).
fibril_length_nm = 1000	inline	Defensible as upper-range AFM value; mean ~615 nm (Yokoi 2005). Flag as upper bound.
RADA16_FIBRILS_PER_CROSSSECTION = 5 (avg)	—	Geometrically plausible (10–20 nm bundle / 3 nm tape width = 3–7 fibers/bundle). Not directly stated in any paper.
K_PROTEOLYSIS = 1.4/h (t½ 30 min)	“conservative”	Wrong regime. For assembled gel, in vivo t½ is 7–14 days → k ≈ 0.002–0.004/h. Model is 350–700× faster than reality in the error-safe direction (overestimates clearance). Need to split: k_gel_dissolution (slow, scaffold at delivery site) vs k_free_monomer_proteolysis (fast, for peptide monomers that haven’t assembled).
118 aa tail on RADA16	core design assumption	NOT IN CHARACTERIZED PARAMETER SPACE. Empirical limit for sequence modification preserving assembly is ~12 residues. Our tail is 10× beyond. Rigorous path: 9:1 molar blend (plain RADA16 : RADA16-tail91) where plain scaffold carries assembly and tail91 displays WH2/TMEM145-binder on surface. Documented in literature for similar hybrids (Gelain osteogenic). Must be added to Phase 4e design.

Critical implication

h09 Phase 3b PEPTIDE_TAIL91 cannot be assumed to self-assemble at 100% composition. Every dose calculation in Phase 4e that treats the entire administered peptide as contributing to the functional scaffold is 10× too optimistic if a 9:1 blend is used (only 10% of mass is functional). Alternatively, if pure tail91 is used, assembly likely fails entirely.

Connections

• [part-of] _hub (literature-params)
• [see-also] cochlear-pkpd (gel dissolution constant conflicts with K_PROTEOLYSIS)
• [see-also] actin-kinetics (avidity argument rests on multi-WH2 per fibril)
• [applies] STRC Synthetic Peptide Hydrogel HTC